Life Sciences Commons^™

Marine Fungi Of U.S. Gulf Of Mexico Barrier Island Beaches: Biodiversity And Sampling Strategy, Allison Kathleen Walker

Dissertations

Marine fungi are an important but often overlooked component of marine ecosystems. Primarily saprotrophic, they are vital to coastal nutrient cycling processes and food webs. However, basic marine fungal distribution data are lacking in many parts of the world, as is knowledge of the sampling intensity required to characterize the biodiversity of these communities. The roles of substrate, season and latitude in shaping intertidal ascomycete community structure were examined for the U.S. Gulf of Mexico, and the role of sampling frequency on species richness estimates was also addressed. Best sampling practices were developed and 750 collections of beach detritus, sand …

Management Of Biological And Chemical Constituents For The Advancement Of Intensive, Minimal-Exchange, Biofloc-Based Shrimp (Litopenaeus Vannamei) Aquaculture, Andrew James Ray

Dissertations

Intensive, minimal-exchange, biofloc-based shrimp aquaculture systems may provide a sustainable alternative to traditional shrimp culture. Through a series of experiments, this document explores the effects of several key management strategies on water quality, isotopic distribution, and shrimp production.

An experiment evaluated the effects of managing suspended solids (biofloc) concentration at two levels. It was found that using a higher flow rate to larger settling chambers resulted in significantly lower biofloc and nitrate concentrations, and significantly improved shrimp growth rate. A second experiment compared systems with clear water and systems with biofloc. The filters in the clear water systems prevented biofloc …

A Time Series Analysis Method Using Hidden Variables For Gene Network Reconstruction, Xi Wu

Dissertations

The DNA microarray technology can be applied to obtain time series data which contains thousands of genes and tens of time points. When confront the great amount of data points a fast and effective method must be constructed to extract useful information. The assumption that the interactions between genes are static in the time series data is made. After made the assumption how to reconstruct those interactions becomes a difficulty problem. Since the underlying interactions between genes are complicated, which involve transcription, translation and protein-protein interaction, to construct a model from physicochemistry is almost impossible/effortless. The popular methods constructed from …

Fluorescence And Size Characterization Of Dissolved Organic Matter In Riverine And Sea Waters In The Northern Gulf Of Mexico, Zhengzhen Zhou

Dissertations

Riverine export of dissolved organic matter (DOM) is an important component in marine carbon budget but the composition and phase partitioning are poorly quantified. Monthly water samples were collected from the lower Mississippi and Pearl rivers between January 2009 to August 2011 for DOM characterization using the fluorescence excitation emission matrix (FluoEEM) technique, coupled with parallel factor analysis (PARAFAC), and flow field-flow fractionation technique. DOM in the Pearl River showed higher dissolved organic carbon (DOC) concentration, temporal fluctuation, and aromaticity, reflecting instantaneous inputs of DOM from local soil and plant litter. In contrast, DOM in the Mississippi River exhibited lower …

The Role Of The Cysteine/Glutathione Regulatory Genes Cdo1, Gsh1, And Gsh2 In Yeast-Mold Dimorphism Of The Pathogenic Fungus Histoplasma Capsulatum, Melissa Anne Adams

Dissertations

The dimorphism of Histoplasma capsulatum (Hc) from a mold to yeast is regulated by many environmental factors such as temperature and thiol concentrations. Histoplasma exists in the soil (or in vitro at 25ºC) as a multicellular saprophytic mold. In the lungs of an infected host (or in vitro at 37ºC), a shift to the unicellular parasitic yeast occurs. Sulfhydryl groups (-SH), especially cysteine, are necessary in the culture medium for the mold to yeast transition. Cysteine is the precursor for the synthesis of glutathione. Enzymes involved in the cysteine metabolism pathway are being studied in order to evaluate …

Clam (Corbicula Fluminea) As A Potential Sentinel Of Human Norovirus Contamination In Freshwater, Xunyan Ye

Dissertations

The purpose of this study was to evaluate and validate the use of the clam Corbicula fluminea as a sentinel of human noroviruses (HuNoV) contamination in freshwater. The first specific aim was to develop a new method to extract HuNoV RNA from contaminated bivalves (e.g. oysters, clams) that would be much faster than existing methods. The procedure developed includes an initial total RNA extraction using TRI Reagent, followed by HuNoV RNA concentration and purification using biotinylated probe-capture technology. HuNoV RNA is finally detected by real-time RT-PCR. Using bivalve homogenates spiked with HuNoV, 100 PCR detection units of the virus was …

Genetic Variation In Potentially Virulent Vibrio Parahaemolyticus From The Northern Gulf Of Mexico, Nicholas Felix Noriea Iii

Dissertations

Vibrio parahaemolyticus (V_p) is a gram-negative bacterium found naturally in marine and estuarine environments. V_p is found in oysters including those which are later consumed by the public. Sub-populations of potentially virulent Vp contain specific virulence factors and are relevant human pathogens capable of causing gastroenteritis, wound infection, and death. The tdh and trh genes, both encoding hemolysins, have been correlated with the majority of clinical V_p isolates but have not been shown to be the definitive virulence factors.

A total of 146 V_p isolates from the northern Gulf of Mexico were collected and probed …

Application Of A Hybrid 3d-Var Data Assimilation System In The Monterey Bay To Study Regional Dynamics Of The California Current System, Chudong Pan

Dissertations

A data assimilation system combining 3-dimensional variational scheme and Navy Coastal Ocean Model was applied to the Monterey Bay area to assimilate temperature and salinity glider data collected in August 2003. The hybrid background error covariance model in the present 3-dimensional variational system incorporates both the static and the flow-dependent background error covariance. To explore the impact of high temporal resolution on the overall skill of the assimilation system, the intended data assimilation interval was set to 1 hour in the present study. A Floating Temporal Window approach is designed to keep the computational efficiency of the scheme and to …

Personality Assessment In African Elephants (Loxodonta Africana), Kristina Marie Horback

Dissertations

The following study assessed personality in twelve African elephants using both observational behavior coding and standardized trait rating methods, thus demonstrating consistent individual differences across time and contexts. During the summer of 2010 and 2011, over 640 hours of behavioral data were collected onsite at the San Diego Zoo Safari Park in Escondido, CA. Four coding-based personality traits were determined after analysis: PLAYFUL, CURIOUS, TOLERANT, and, AGGRESSIVE. This data was then compared to survey ratings completed by the animal keeper staff during both summers. Four rating-based personality traits resulted from this analysis: PLAYFUL, CURIOUS, TIMID, and, AGGRESSIVE. All eight composite …

Effects Of Hypoxia And 4-Tert-Octylphenol On Gene Expression Profiles Of The Sheepshead Minnow (Cyprinodon Variegatus), Arthur Alan Karels

Dissertations

Hypoxia occurs in estuaries of northern Gulf of Mexico and world-wide, with increasing frequency/severity via eutrophication and anthropogenic influences. Hypoxia inducible factors (HIFs) form transcriptional complex and bind DNA at hypoxia responsive elements (HREs) in promoter regions of genes needed for systemic and cellular adaptation of fish to low dissolved oxygen (hypoxia, DO <2.0 mg/ml). Hypoxia-induced activation of HIF-αs can lead to a cascade of downstream activation, such as erythropoietin (EPO). Return to normal DO levels (normoxia), prolyl hydroxylases (PHDs) are activated to degrade HIF-αs back to baseline. Fish are affected by environmental estrogen mimics, like 4-tert-octylphenol (4tOP), binding estrogen receptor alpha (ERα) at estrogen responsive elements (EREs) and activating genes vitellogenin (VTG). Previous research showed overlap or crosstalk between these two mechanistic pathways. Hypoxia triggers unknown factors regulating ERE-mediated ERα signaling pathway, and stressor combinations could increase/decrease hypoxic or endocrine pathway. Research examined molecular/physiological effects of hypoxia (acute and chronic, moderate and severe) and 4tOP (~60μg/L)on adult male and/or female sheepshead minnow (Cyprinodon variegatus). Three genes identified, cloned, and sequenced (HIF-1α, HIF-2α, and PHD3), plus previously identified genes EPO and VTG, were examined in liver/testes exposed to hypoxia and/or 4tOP for cellular/physiological changes. Endpoints examined included mRNA expression from real-time PCR of HIF-1α, HIF-2α, PHD3, EPO, and VTG using cDNA from total RNA extracts, and microarray analyses of genes expressed during the transition from hypoxia back to normoxia. Phylogenetic analyses confirmed isolation of two HIF-α isofoms (HIF-1α and HIF-2α) and the PHD3 isoform. Significant up-regulation of PHD3 occurred within 10 hrs of chronic hypoxia, and persisted when severe (1.5 mg/L) and declined when moderate (~2.5mg/L). Significant up-regulation of HIF-1α and EPO occurred within 30 minutes to 2 hours of onset of acute severe and very severe (~1.08mg/L) hypoxia. Hypoxia acted similar to an estrogen mimic, with huge up-regulation of VTG gene expression in males, and increased VTG levels (additive effect) when hypoxia was combined with 4tOP. Microarray analyses showed 125 genes with significant transcriptional change, with up- or down-regulation from transitions of: (1) hypoxia (72 hrs) to normoxia (74 hrs) and (2) hypoxia+4tOP (72 hrs) to normoxia+4tOP (74 hrs).